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Thursday, February 19, 2015

Up for public comment at bioRxiv this week is this paper on the population history of the Near East, with a special focus on Armenians. Here's the abstract:

The Armenians are a culturally isolated population who historically inhabited a region in the Near East bounded by the Mediterranean and Black seas and the Caucasus, but remain underrepresented in genetic studies and have a complex history including a major geographic displacement during World War One. Here, we analyse genome-wide variation in 173 Armenians and compare them to 78 other worldwide populations. We find that Armenians form a distinctive cluster linking the Near East, Europe, and the Caucasus. We show that Armenian diversity can be explained by several mixtures of Eurasian populations that occurred between ~3,000 and ~2,000 BCE, a period characterized by major population migrations after the domestication of the horse, appearance of chariots, and the rise of advanced civilizations in the Near East. However, genetic signals of population mixture cease after ~1,200 BCE when Bronze Age civilizations in the Eastern Mediterranean world suddenly and violently collapsed. Armenians have since remained isolated and genetic structure within the population developed ~500 years ago when Armenia was divided between the Ottomans and the Safavid Empire in Iran. Finally, we show that Armenians have higher genetic affinity to Neolithic Europeans than other present-day Near Easterners, and that 29% of the Armenian ancestry may originate from an ancestral population best represented by Neolithic Europeans.

Unfortunately, the authors failed to even mention the main cause of what they're seeing; the massive influx of Ancient North Eurasian (ANE) admixture into the Near East. They included ancient genomes Oetzi the Iceman and La Brana-1 in their analysis, but not MA-1 or Mal'ta boy, the main ANE proxy.

MA-1 is a low coverage genome, and not easy to work with, but until better ANE reference genomes are sequenced, it simply can't be ignored in studies on the population history of West Eurasia. Here's why:

Above is my Fateful Triangle PCA. Note the eastern shift of the Islamic Near Eastern groups relative to their non-Islamic neighbors. Here are the relevant ANE ancestry proportions:

Anatolian Turks ~16.54%Armenians ~15.48%

Iranians ~19.61%Iranian Jews ~14.01%

Lebanese Muslims ~9.82%Lebanese Christians ~7.14%

The differences aren't very dramatic, but they're consistent and, as per the PCA, hard to overlook. Indeed, the contrast would be even more obvious if we were to add to the list other exotic admixtures, such as East Asian, South Asian and/or Sub-Saharan.

If you're wondering why it is that Muslims generally carry more ANE than their non-Muslim neighbors, it's probably because the Islamic expansion had a homogenizing effect on the Near East, and it didn't have as much of an impact on the religious minorities in the region.

How and when ANE arrived in the Near East is still a mystery which can only be solved with ancient DNA. However, my bet is that most of it came after the Neolithic from the Eurasian steppe, the northeast Caucasus and the Altai, with the Indo-Europeans, Kura-Araxes people and Turks, respectively.

Tuesday, February 17, 2015

Most of the action on this blog in recent weeks has revolved around the Indo-European urheimat question. So it's probably not a coincidence that I just got this press release in the mail:

Linguists have long agreed that languages from English to Greek to Hindi, known as 'Indo-European languages', are part of a language family which first emerged from a common ancestor spoken thousands of years ago. Now, a new study gives us more information on when and where it was most likely used. Using data from over 150 languages, linguists at the University of California, Berkeley provide evidence that this ancestor language originated 5,500 - 6,500 years ago, on the Pontic-Caspian steppe stretching from Moldova to Russia and western Kazakhstan.

"Ancestry-constrained phylogenetic analysis supports the Indo-European steppe hypothesis", by Will Chang, Chundra Cathcart, David Hall and Andrew Garrett, will appear in the March issue of the academic journal Language. A pre-print version of the article is available on the LSA website [see HERE].

This article provides new support for the "steppe hypothesis" or "Kurgan hypothesis", which proposes that Indo-European languages first spread with cultural developments in animal husbandry around 4500 - 3500 BCE. (An alternate theory proposes that they spread much earlier, around 7500 - 6000 BCE, in Anatolia in modern-day Turkey.)

Chang et al. examined over 200 sets of words from living and historical Indo-European languages; after determining how quickly these words changed over time through statistical modeling, they concluded that the rate of change indicated that the languages which first used these words began to diverge approximately 6,500 years ago, in accordance with the steppe hypothesis.

This is one of the first quantitatively-based academic papers in support of the steppe hypothesis, and the first to use a model with "ancestry constraints" which more directly incorporate previously discovered relationships between languages. Discussion of prior studies in favor of and against the steppe hypothesis can be found in the paper.

I'm reading the paper now, and it'll probably take me a while to get my head around it. Admittedly, linguistics is not my strong point, but I might post some observations in the comments if I feel up to it.

In any case, here's one of the phylogenetic trees from the paper. It'd be interesting to see how it lines up with thousands of complete Y-chromosome sequences from these language groups, particularly from Y-haplogroup R1; I have a feeling we'd see some very nice correlations.

Thursday, February 12, 2015

The main angle of the recently released epic manuscript Haak et al. 2015 is that ancient DNA supports the steppe origin of at least some of Europe's Indo-European languages. That's certainly a move in the right direction, so that we can eventually do away with the Anatolian hypothesis, which was always a failed proposition.

But it's clear that the authors are holding back. They've obviously decided to be very cautious until they've looked at more ancient DNA, particularly from the Near East, Central Asia and India, before backing fully any one Proto-Indo-European (PIE) urheimat model.

That's understandable, considering how much opposition there is still to the steppe hypothesis, even though it does by and large have the support of historical linguists, which is what really counts. Nevertheless, my feeling is that Haak et al. are underselling their data, particularly the stuff from Eastern Europe.

I'm of the opinion that the steppe or Kurgan PIE model works just fine, and also not surprised by the ancient DNA evidence pointing to a massive expansion of people from the western steppe during the Late Neolithic/Early Bronze Age. So for me, the really big news in this paper is that the only two Eastern European forager samples belong to basal lineages of Y-chromosome haplogroups R1a and R1b. What this suggests, Id' say, is that ancient Eastern Europe was a key bifurcation region for R1.

Remarkably, it's possible to basically lay out the history and phylogeny of R1a in Europe using just three R1a samples from the paper. This can't be a coincidence.

What we can see there is the progression from a basal R1a in pre-Neolithic Northeastern Europe to a derived R1a in late prehistoric Central Europe. The derived R1a is actually R1a1a1b1a2, which is by far the most common subclade of R1a in Europe today, and closely related to the Asian and Indo-Iranian-specific R1a1a1b2.

Interestingly, all seven of the Yamnaya males sampled by Haak et al., mostly from the Samara Valley, belong to R1b-M269, the most common subclade of R1b today. However, five belong to the West Asian-specific R1b-Z1203, but none to the West European-specific R1b-M412. Also, all nine Yamnaya samples show Near Eastern admixture, described in the paper as Armenian-like.

Does this perhaps mean that the Proto-Indo-Europeans (and thus Yamnaya) originated in the Near East, as per the Armenian Plateau hypothesis?

I doubt it. The aforementioned Eastern European R1b forager is also from the Samara Valley, and he clearly lacks Near Eastern admixture. So what are the chances that a Near Eastern population with a frequency of R1b-M269 of around 100% moved into an area of Eastern Europe where a more basal R1b was already present, and in fact in a population with no Near Eastern ancestry? Very slim, I'd say.

So how did the Yamnaya herders acquire their Near Eastern admixture? The answer is obvious if we look at their mtDNA haplogroups. These include H, T and W, all of which might have come to Eastern Europe from the Near East.

Of course this doesn't mean that the Eastern European steppe was overrun by Near Eastern Amazons. It's generally accepted that during the Neolithic the steppe was settled by farmers from the Near East, just like much of the rest of Europe, and I'd say that it was mostly the women from these groups who were incorporated into the later pastoralist societies of the steppe. The men, who probably belonged to Near Eastern haplogroups like G or T, might have been killed or marginalized in some way, so that their reproductive success was seriously hampered.

This is not a far fetched scenario. Typical hunter-gatherer Y-haplogroups like I2 and C6 have already been recorded alongside Near Eastern-specific mtDNA lineages at several Neolithic sites in Western and Central Europe. The social mechanisms for this might have been different there than on the steppe, but in any case, it seems that European hunter-gatherer males shacking up with farm girls of largely Near Eastern ancestry was not an unusual occurrence back in the day.

Now, if Eastern Europe was indeed a bifurcation hotspot for R1, then a large proportion, or even the majority of R1a and R1b in Eurasia today, might well be of Eastern European origin. If so, there should be some support for this in genome-wide DNA of present-day Asians, and indeed I think there is.

Below are a couple of principal component analyses (PCA). The first is from Haak et al. and the second from my own West Eurasia K8 analysis (see here). Unfortunately, I don't yet have access to the Yamnaya genomes, but I think it's petty easy to guesstimate where they will land on my plot when I run them in the K8. I marked this spot with an X.

Note that most of the Near Eastern and Caucasian populations are clearly shifted east towards ANE, and also up towards Europe. Moreover, I'd say many of these groups are specifically pushing up towards the Volga-Ural samples and thus the Yamnaya herders.

There's really no other way to explain this outcome. Quite simply, the vast majority of West Asians have relatively recent (post-Neolithic?) ancestry from the Ural or Kazakh steppe, which manifests itself as a west to east cline on PCA, running from the southern Levant to the north Caucasus. This result is easily reproduced on any decent PCA with West Eurasian populations, and can be seen on the Haak et al. plot.

I'm yet to find solid evidence that Indo-European speakers from the Near East, like Armenians, Kurds and Iranians, don't harbor fairly significant ancestry from this northeastern source.

For instance, unlike many people, I don't find unsupervised ADMIXTURE analyses very convincing when they show these groups to be entirely of Near Eastern ancestry. That's because when ADMIXTURE creates a modern Near Eastern/West Asian cluster, it usually lumps within it all of the ancient ancestral components that are today ubiquitous in the Near East. In other words, the steppe admixture which shows up amongst most West Asians on the PCA above is classified as native to the Near East, even though this is unlikely to be true.

Tuesday, February 10, 2015

I'll probably end up writing a whole series of posts on this paper. But for now, here's the abstract and a PCA.

We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost four hundred thousand polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of western and far eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary, and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000 year old Siberian6. By ~6,000-5,000 years ago, a resurgence of hunter-gatherer ancestry had occurred throughout much of Europe, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ~3/4 of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ~3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for the theory of a steppe origin of at least some of the Indo-European languages of Europe.

Monday, February 9, 2015

Harvard Professor David Reich is holding a seminar later today at Jesus College, Oxford, on the population history of Europe. Part of the talk will focus on unpublished genome-wide data from 69 ancient remains from Germany, Hungary, Russia and Spain, as far as I know mostly dating to 6,000-1,000 BC (see here).

I'm hoping that Professor Reich might also reveal a few details, or at least give us some clues, about the Y-haplogroups of these prehistoric individuals. It would be interesting to find out, for instance, which of the samples belong to R1b, the most common Y-haplogroup in Europe today, but thus far missing from ancient European DNA older than the late Neolithic.

It's likely that some of the people attending the seminar will blog or tweet about it soon after it's over. I'll try to compile the most useful of these reports in an update tomorrow. Feel free to help me out in the comments section below. However, please keep the discussion firmly on topic.

Update 09/02/2015: Jean Manco, author of the recent book Ancestral Journeys, is sharing her notes from the lecture here. Paraphrasing David Reich, she says that Yamnaya brought both R1a and R1b to Europe.

Friday, February 6, 2015

If anyone reading this is going to the Annual Meeting of the American Association of Physical Anthropologists (AAPA) in St. Louis next month, I'd love to know what was said at the following presentations.

The origins of the Aegean palatial civilizations from a population genetic perspective

The present paper investigates the origins of the Aegean pre-palatial civilizations (5th-3rd millennium BC) by applying cutting-edge methods of molecular biology and population genetics. The term Aegean Civilizations refers to the novel human lifeway (agriculture and craft specialization, redistribution systems, intensive trade) that appeared during the end of the
Neolithic and the beginning of the Bronze Age in the Aegean. Although many studies exist on archaeological constructions of ethnic and cultural identity on mainland Greece, the Cyclades and Crete, not enough efforts have been made to explore this direction on a population history basis. We have investigated Late, Final Neolithic and Early Bronze Age human skeletons (n=127) from the Aegean using ancient DNA methods, next generation sequencing (NGS) technology and statistical population genetic inferences to i) gather information on diversity, population size, and origin of the pre-palatial Aegean Cultures, ii) to compare them on a genetic basis, in terms of their cultural division (Helladic, Cycladic, Minoan) and iii) to investigate their ancestral/non-ancestral status to the Early and Middle Neolithic farmers from Greece. In addition to mitochondrial DNA genomes, by applying a capture-NGS approach we collected information on functional traits of the early Aegean communities in southeastern Europe. Considering the International Spirit that overwhelms the Aegean during the 3rd millennium BC, seen by the wide distribution of artifacts, this palaeogenetic approach provides valuable new insights on population structure of the groups involved in the Neolithic-Bronze Age transition and the spread of specific alleles in this part of Europe.

One of the most exciting consequences of recent developments in ancient DNA technology is that we have the ability to infer the phenotypes of ancient samples for traits that cannot be reliably inferred from skeletal remains. Important examples include pigmentation traits, dietary traits like lactase persistence and amylase copy number, and disease resistance mutations. These have relatively simple genetic architectures, but by using information from genome-wide association studies, and by genotyping many more sites, we can also predict the values of polygenic traits that are controlled by many loci, for example height, weight, and complex disease susceptibility. By investigating how they change through time, we can disentangle the effects of natural selection and population turnover in the evolution of these traits. In this study, we present genetic data from a series of samples from seven archaeologically defined cultures in central Europe, ranging from 8000BCE to present. We have genotyped these samples at 390,000 genomic loci, including 30,000 which have known phenotypic effects. We then use this data to distinguish between traits that have changed consistently with population turnovers, traits that have changed apparently neutrally, and traits that have changed dramatically due to recent natural selection. Finally, we investigate whether we can detect selection in polygenic traits like height or weight. These data demonstrate a powerful new source of information about ancient samples, and have the potential to teach us both about the specific traits of these populations, and also about the general mechanisms of evolution and adaptation in human history.

Also worthy of note is this talk on ancient genomes from the Peruvian Andes. The study appears to be another nail in the coffin of old school physical anthropology.

Genome-wide data from ancient Peruvian highlanders and the Population History of South America

Despite recent advances in archaeology and population genetics, the number of human dispersals into South America and the routes these settlers took throughout the continent remains subject to controversy. The analysis of DNA from ancient human remains has proven to be an efficient tool to get insights into such ancient population dynamic processes. However, ancient DNA research in South America so far has been mostly restricted to the analysis of the mitochondrial control region and samples 5000
years old and younger. While these studies have increased our understanding of the pre- Columbian population history, inferences have been restricted to female population dynamics and have not allowed us to address relevant aspects like admixture and selection properly. Here, we present genome wide data from pre-Columbian Central Andean individuals from various archaeological sites dating from 7000 BC to 1100 AD. Ancient DNA genomic libraries were analyzed employing both shotgun sequencing and targeted hybridization capture approaches. We compare this data with published genome-wide data from ancient and modern Native American populations and reconcile our results with craniometric studies. Our results show a striking genetic continuity in the Andes over at least 8000 years despite observed changes in cranio-morphological variability. Additionally, our observations support the hypothesis of a single-wave scenario, in which the early and later populations of pre- Columbian South America derived primarily from a single source population.

The AAPA 2015 website is here. You can download a PDF book with all of the abstracts here.